Commit d08f13be authored by zhanxw's avatar zhanxw
Browse files

update boltCov doc

parent 67861457
......@@ -7,6 +7,10 @@
* Fix strtol related warning (possibly) (refer to #33)
* Clean codes
2017-04-27 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add boltCov model
2017-04-14 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a critical bug related to AF calculation (issue 15)
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......@@ -291,13 +291,20 @@ Score test | score | B,Q | Y | R, U
Dominant model | dominant | B,Q | Y | R, U | score tests and covariance matrix under dominant disease model
Recessive model | recessive | B,Q | Y | R, U | score tests and covariance matrix under recessive disease model
Covariance | cov | B,Q | Y | R, U | covariance matrix
BOLT-LMM score test | score[bolt] | Q | Y | R, U | BOLT-LMM based score tests
BOLT-LMM score test | bolt | Q | Y | R | BOLT-LMM based score tests (###)
BOLT-LMM covariance | boltCov | Q | Y | R | BOLT-LMM based score tests (###)
(#) Model columns list the recognized names in rvtests. For example, use `--meta score,cov` will generate score statistics and covariance matrix for meta-analysis.
(##) In trait column, B or Q stand for binary or quantitative trait, respectively.
(###) This method also requires pruned gneotype data in the PLINK format specified by `--boltPlink`. A minimal example to run BOLT-LMM based score tests is: `rvtest --inVcf $inputVCFfile --boltPlink $binaryPlinkPrefix --pheno $phenotype --meta score[bolt]`.
(###) This is an experimental feature.
This method requires LD-pruned gneotype data in the binary PLINK format specified by `--boltPlink`.
A minimal example to run BOLT-LMM based score tests is: `rvtest --inVcf $inputVCFfile --boltPlink $binaryPlinkPrefix --pheno $phenotype --meta bolt`.
To prune your genotype data, an example command line is `plink --vcf $inputVCFFile --maf 0.05 --indep-pairwise 50 5 0.5 --make-bed $binaryPlinkPrefix`.
Please note RVTESTS additionally prohibit duplicated rs IDs in the PLINK BIM file.
To remove duplications, you can list all duplicated `cut -f2 $binaryPlinkBIMfile|sort |uniq -d > duplicate.rsid`, and then
use `plink --vcf $inputVCFFile --maf 0.05 --indep-pairwise 50 5 0.5 --exclude duplicate.rsid --make-bed $binaryPlinkPrefix`.
The above models are suitable to generate summary statistics which can be later meta-analyzed (see [Dajiang Liu (2014) Nature Genetics](http://www.nature.com/ng/journal/v46/n2/abs/ng.2852.html)).
Rvtests implemented the above methods and the results can be further analyzed by RareMetals ([link](http://genome.sph.umich.edu/wiki/RareMETALS)) for quantitative trait and RareMetals2 ([link](http://genome.sph.umich.edu/wiki/RareMETALS2)).
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